Pardo-Avila F - Search Results

1

Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome.

Di Palma F, Decherchi S, Pardo-Avila F, Succi S, Levitt M, von Heijne G, Cavalli A. Di Palma F, et al. Among authors: pardo avila f. J Chem Theory Comput. 2022 Mar 8;18(3):1905-1914. doi: 10.1021/acs.jctc.1c00796. Epub 2021 Dec 9. J Chem Theory Comput. 2022. PMID: 34881571 Free PMC article.

2

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

Kudva R, Tian P, Pardo-Avila F, Carroni M, Best RB, Bernstein HD, von Heijne G. Kudva R, et al. Among authors: pardo avila f. Elife. 2018 Nov 26;7:e36326. doi: 10.7554/eLife.36326. Elife. 2018. PMID: 30475203 Free PMC article.

3

Millisecond dynamics of RNA polymerase II translocation at atomic resolution.

Silva DA, Weiss DR, Pardo Avila F, Da LT, Levitt M, Wang D, Huang X. Silva DA, et al. Proc Natl Acad Sci U S A. 2014 May 27;111(21):7665-70. doi: 10.1073/pnas.1315751111. Epub 2014 Apr 21. Proc Natl Acad Sci U S A. 2014. PMID: 24753580 Free PMC article.

4

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models.

Zhang L, Pardo-Avila F, Unarta IC, Cheung PP, Wang G, Wang D, Huang X. Zhang L, et al. Acc Chem Res. 2016 Apr 19;49(4):687-94. doi: 10.1021/acs.accounts.5b00536. Epub 2016 Mar 18. Acc Chem Res. 2016. PMID: 26991064 Free PMC article.

5

Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature.

O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H. O'Sullivan ME, et al. Among authors: pardo avila f. Nucleic Acids Res. 2018 Oct 12;46(18):9793-9804. doi: 10.1093/nar/gky693. Nucleic Acids Res. 2018. PMID: 30113694 Free PMC article.

6

Comprehensive computational design of ordered peptide macrocycles.

Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D. Hosseinzadeh P, et al. Among authors: pardo avila f. Science. 2017 Dec 15;358(6369):1461-1466. doi: 10.1126/science.aap7577. Science. 2017. PMID: 29242347 Free PMC article.

7

Structure of the 30S ribosomal decoding complex at ambient temperature.

Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. Dao EH, et al. Among authors: pardo avila f. RNA. 2018 Dec;24(12):1667-1676. doi: 10.1261/rna.067660.118. Epub 2018 Aug 23. RNA. 2018. PMID: 30139800 Free PMC article.

8

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase.

Da LT, Pardo Avila F, Wang D, Huang X. Da LT, et al. PLoS Comput Biol. 2013 Apr;9(4):e1003020. doi: 10.1371/journal.pcbi.1003020. Epub 2013 Apr 4. PLoS Comput Biol. 2013. PMID: 23592966 Free PMC article.

9

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

Da LT, Pardo-Avila F, Xu L, Silva DA, Zhang L, Gao X, Wang D, Huang X. Da LT, et al. Nat Commun. 2016 Apr 19;7:11244. doi: 10.1038/ncomms11244. Nat Commun. 2016. PMID: 27091704 Free PMC article.

10

8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II.

Konovalov KA, Pardo-Avila F, Tse CKM, Oh J, Wang D, Huang X. Konovalov KA, et al. Among authors: pardo avila f. J Biol Chem. 2019 Mar 29;294(13):4924-4933. doi: 10.1074/jbc.RA118.007333. Epub 2019 Feb 4. J Biol Chem. 2019. PMID: 30718278 Free PMC article.

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